We noticed a "bug" in the new PL/SQL Developer Version 13. There in the "window list" regarding the compilation flag. The issue is reproduceable with following steps.
1) Set main connection to 'ConA'.
2) Open a package and set its connection to 'ConB' (other than the main connection).
3) After compilation of this package, the compilation flag disappears.
4) Open another package and change its connection from the main connection to 'ConB' as well.
5) At this time, the compilation flag of the first package appears again. Even though it has been compiled already and remained unchanged.